mcDETECT 2.0.10__py3-none-any.whl → 2.0.11__py3-none-any.whl

mcDETECT/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.0.10"
+__version__ = "2.0.11"
 
 from . import model
 from . import utils

mcDETECT/model.py

@@ -122,10 +122,21 @@ class mcDETECT:
                     continue
                 temp_in_nucleus = np.sum(target["overlaps_nucleus"].values[mask])
                 temp_size = coords.shape[0]
-                # coords_unique = np.unique(coords, axis=0)
+                
                 temp = pd.DataFrame(coords, columns=["global_x", "global_y", "global_z"])
                 temp = temp.drop_duplicates()
-                center, r2 = miniball.get_bounding_ball(np.array(temp), epsilon=1e-8)
+                coords_unique = temp.to_numpy()
+                if coords_unique.shape[0] < self.low_bound:
+                    print(f"Skipping small cluster for gene {j}, cluster {k} (n = {coords_unique.shape[0]})")
+                    continue
+                try:
+                    center, r2 = miniball.get_bounding_ball(coords_unique, epsilon=1e-8)
+                except np.linalg.LinAlgError:
+                    print(f"Warning: singular matrix for gene {j}, cluster {k} —- using fallback sphere.")
+                    center = coords_unique.mean(axis=0)
+                    dists = np.linalg.norm(coords_unique - center, axis=1)
+                    r2 = (dists.max() ** 2)
+                
                 if self.type != "Xenium":
                     closest_z = closest(z_grid, center[2])
                 else:

{mcdetect-2.0.10.dist-info → mcdetect-2.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mcDETECT
-Version: 2.0.10
+Version: 2.0.11
 Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
 Home-page: https://github.com/chen-yang-yuan/mcDETECT
 Author: Chenyang Yuan

mcdetect-2.0.11.dist-info/RECORD

@@ -0,0 +1,8 @@
+mcDETECT/__init__.py,sha256=8ZH_Aljm3rgizWtNHOlZMSrmaALRJwLuiyygwrgEWAk,93
+mcDETECT/model.py,sha256=VskA4YKQ9-16AB-Le6HdWNEwyNoQiFxIckCZ8xR8HiY,29950
+mcDETECT/utils.py,sha256=0gvqZV7sGi8qvvdC5x9XScyiTXlSfqbUt1zks4t7Xd4,4545
+mcdetect-2.0.11.dist-info/licenses/LICENSE,sha256=uxq-shEWOGTIGVnQLmpElILmfCkuUhFZRAMnZUiKvtg,1070
+mcdetect-2.0.11.dist-info/METADATA,sha256=BCb4S7JuBZCUq3wpyHbW4rhjRGKjmLi-lhLkLzAoTgE,3017
+mcdetect-2.0.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+mcdetect-2.0.11.dist-info/top_level.txt,sha256=WwzBojt5U-T2hZ8llO6XgpM9OFIBkWQQldQKu19O8EY,9
+mcdetect-2.0.11.dist-info/RECORD,,

mcdetect-2.0.10.dist-info/RECORD

@@ -1,8 +0,0 @@
-mcDETECT/__init__.py,sha256=FoRKnIon2qyKVkAcetKJDkIw8YuDuM1LhpoCZv-AE38,93
-mcDETECT/model.py,sha256=oEkBpFPZWBTRScjsyfwes6oTu6hDsjsI-MCVdVxGiFk,29375
-mcDETECT/utils.py,sha256=0gvqZV7sGi8qvvdC5x9XScyiTXlSfqbUt1zks4t7Xd4,4545
-mcdetect-2.0.10.dist-info/licenses/LICENSE,sha256=uxq-shEWOGTIGVnQLmpElILmfCkuUhFZRAMnZUiKvtg,1070
-mcdetect-2.0.10.dist-info/METADATA,sha256=N8RO2SHnwLe-LZ1wEu1xFTumQ_u4mTfMEdF8exePRYM,3017
-mcdetect-2.0.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-mcdetect-2.0.10.dist-info/top_level.txt,sha256=WwzBojt5U-T2hZ8llO6XgpM9OFIBkWQQldQKu19O8EY,9
-mcdetect-2.0.10.dist-info/RECORD,,